RetrogeneDB ID: retro_ecab_539

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 20:28812167..28812580(+)
• Located in intron of: ENSECAG00000013642

Retrocopy information

• Ensembl ID: ENSECAG00000013675
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: YBX1
• Ensembl ID: ENSECAG00000023592
• Aliases: None
• Description: Y box binding protein 1 [Source:HGNC Symbol;Acc:8014]

Sequence

>retro_ecab_539
AGGCCCTACCGCAGGCAACGGTTCCCACCTTACTACATGCGGAGACCCTATGGGCGTCGACCACAGTATTCCAACCCTCC
TGTGCAAGGAGAAGTGATGGAGGGTGCTGACAACCAGGGTGCAAGAGAACAAGGTAGACCAGTGAGGCAGAATATGTATC
GGGGTTGTACACCACGATTCCGCAGGGGCCCTCCTCGCCAAAACAGCCTAGAGAGGATGGCAATGAAGATAAGGAAAATC
AAGAAGATGAGACCCAAGGTCAGCAGCCACCTCAACGTCGGTACCGCCGCAACTTCAATTACCTACGCAGACGCCCAGAA
ATCCCTAAACCACAAGATGGCAAAGAGACAAAAGCAGCCGATCCACCAGCTGAGAATTCCTCCGCTCCCGAGGCTGGGCA
GGGCGGGGCTGAG

Alignment

ORF - retro_ecab_539 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.14 %
• Parental protein coverage: 51.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RPYRRRRFPPYYMRRPYGRRPQYSNPPVQGEVMEGADNQGAGEQGRPVRQNMYRGYRPRFRRGPPRQ-RQ
          RPYRR.RFPPYYMRRPYGRRPQYSNPPVQGEVMEGADNQGA.EQGRPVRQNMYRG..PRFRRGPPRQ..Q
Retrocopy RPYRRQRFPPYYMRRPYGRRPQYSNPPVQGEVMEGADNQGAREQGRPVRQNMYRGCTPRFRRGPPRQ<KQ

Parental  PREDGNEEDKENQGDETQGQQPPQRRYRRNFNYRRRRPENPKPQDGKETKAADPPAENSSAPEAEQGGAE
          PREDGN.EDKENQ.DETQGQQPPQRRYRRNFNY.RRRPE.PKPQDGKETKAADPPAENSSAPEA.QGGAE
Retrocopy PREDGN-EDKENQEDETQGQQPPQRRYRRNFNYLRRRPEIPKPQDGKETKAADPPAENSSAPEAGQGGAE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP021940_articular_cartilage	0.12 RPM	10.92 RPM
SRP021940_cerebellum	0.10 RPM	7.69 RPM
SRP021940_embryo	0.20 RPM	26.72 RPM
SRP021940_placental_villous	0.00 RPM	9.77 RPM
SRP021940_synovial_membrane	0.19 RPM	16.99 RPM
SRP021940_testis	0.38 RPM	67.59 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_539 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_539 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_539 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 54 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000023592	20 retrocopies	retro_ecab_194, retro_ecab_228, retro_ecab_324, retro_ecab_389, retro_ecab_461, retro_ecab_538, retro_ecab_539 , retro_ecab_712, retro_ecab_736, retro_ecab_756, retro_ecab_950, retro_ecab_963, retro_ecab_964, retro_ecab_965, retro_ecab_966, retro_ecab_982, retro_ecab_983, retro_ecab_984, retro_ecab_985, retro_ecab_992,
Loxodonta africana	ENSLAFG00000007597	1 retrocopy	retro_lafr_804,
Macaca mulatta	ENSMMUG00000013136	5 retrocopies	retro_mmul_1139, retro_mmul_1423, retro_mmul_2017, retro_mmul_423, retro_mmul_861,
Oryctolagus cuniculus	ENSOCUG00000028047	2 retrocopies	retro_ocun_1519, retro_ocun_1953,
Otolemur garnettii	ENSOGAG00000006784	25 retrocopies	retro_ogar_1127, retro_ogar_1246, retro_ogar_1350, retro_ogar_1371, retro_ogar_1497, retro_ogar_2011, retro_ogar_2018, retro_ogar_2302, retro_ogar_2359, retro_ogar_2607, retro_ogar_2654, retro_ogar_3170, retro_ogar_3225, retro_ogar_324, retro_ogar_3303, retro_ogar_3316, retro_ogar_3317, retro_ogar_3366, retro_ogar_3416, retro_ogar_3474, retro_ogar_448, retro_ogar_572, retro_ogar_678, retro_ogar_690, retro_ogar_753,
Sorex araneus	ENSSARG00000007896	1 retrocopy	retro_sara_559,